Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of UPR gene expression in the bZIP28 and bZIP60 double mutant dm

ABSTRACT: Understanding the functional roles of bZIP28 and bZIP60 in Arabidopdis

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jian-Xiang Liu

PROVIDER: E-MTAB-2657 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

xve expression

Project description:Understanding the downstream genes regulated by transcription factor MTF1 using inducible promoter system in Arabidopdis

2014-11-16 | E-MTAB-1377 | biostudies-arrayexpress

Alternative RNA processing events in a double NSR mutant Arabidopsis

Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome. RNA-seq experiments (polyA+ RNA) in triplicates for each condition WT and nsrab mutants.

2016-07-03 | E-GEOD-65717 | biostudies-arrayexpress

Transcription profiling of maize segmental aneuploid to study phenotypic and gene expression changes associated with aneuploidy

Project description:ABSTRACT: BACKGROUND: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated. RESULTS: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that ~40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage. CONCLUSIONS: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions. Experiment Overall Design: There are four biological replicates of pooled wild-type siblings and four biological replicates of pooled DpDf plants. The DpDf plants are segmental aneuploids that contain three copies of the short arm of chromosome 5. These plants are all in the B73 inbred genetic background.

2008-06-11 | E-GEOD-10243 | biostudies-arrayexpress

Transcriptional profiling of Arabidopsis thaliana wild type and ip28-2 mutant seedlings treated or mock treated by tunicamycin.

Project description:compare the effect of tunicamycin on gene expression between wild type and zip28-2 mutant

2010-03-01 | E-MEXP-2519 | biostudies-arrayexpress

ire1 double mutant vs wild-type in response to tunicamycin

Project description:Arabidopsis thaliana wild-type and ire1a/ire1b double mutant plants were treated with tunicamycin. RNA was extracted and subjected to microarray analysis.

2012-03-13 | E-MEXP-3186 | biostudies-arrayexpress

Global Functional Targets of the Histone Methyltransferase SDG8 Uncover a Role for Histone Modification in Energy Metabolism

Project description:Histone methylation modulates gene expression in response to external and internal cues. We uncovered a non-redundant role for the Arabidopsis histone methyltransferase, SDG8, which provides a unique opportunity to study the global function of a specific histone methyltransferase within in a multicellular organism. We previously used a promoter responsive to light and carbon in a positive genetic screen to identify an Arabidopsis carbon and light insensitive mutant cli186. In this study, we characterize the mutant cli186 as a complete deletion of a histone methyltransferase gene SDG8 (now renamed sdg8-5). To assess the global role of SDG8, we compared the global histone methylation patterns and the transcriptome of sdg8-5 to wild type (WT) in the context of a transient carbon and light treatment. We showed that the complete deletion of SDG8 in sdg8-5 is associated with a dramatic reduction of H3K36me3 towards the 3’ of the gene body, which correlates with significant reduction in gene expression. We uncovered 1,084 “high confidence” functional targets of SDG8 – affected in both H3K36me3 marks and gene expression – that are associated with specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 71% of these functional targets are responsive to carbon and/or light. Our model suggests that SDG8 functions to mark specific sets of genes with H3K36me3 in the gene body for active transcription, to tune genes involved in primary metabolism that are responsive to the energy level in the environment. Wild type Arabidopisis and sdg8-5 plants were grown in hydroponics system for three weeks, then starved for carbonhydrate and light for 24 h. They were then treated with carbon and/or light or remained untreated as controls.Three biological replicates were collected, resulting in 24 samples (2 genotypes X 2 carbonhydrate treatmens X 2 light treatments X3 biological replicates).

2015-03-01 | E-GEOD-62435 | biostudies-arrayexpress

Transcriptome analysis of ire1 mutants after treatment with or without tunicamycin in the presence of actinomycin D

Project description:Arabidopsis seedlings of wildtype or ire1a ire1b double mutant were treated with or without tunicamycine in the presence of actinomycin D (ActD). 12 samples

2013-03-19 | E-GEOD-39690 | biostudies-arrayexpress

Q0990.bdl vs Q0990.Col

Project description:Transcriptional profiling of Q0990 x bdl vs Q0990 x Col-0 development embryos after 3days and 6 days of fertilization Two conditional experiments: Q0990 x bdl vs Q0990 x Col-0, and two satges was compared: 3days and 6 days after fertilization. . 4 biological replicates for each experiment. The submitter states that the Agilent Feature Extraction files have been lost: the original files was stored in a unrecoverable crashed computer, because the Base 2 in my institute is not in service anymore, so I can not re-download my file with the Agilent Feature

2016-02-26 | E-GEOD-78695 | biostudies-arrayexpress

Using natural variation Drosophila to discover previously unknown ER stress genes

Project description:To measure natural variation in ER stress transcriptional response in a subset of lines from the Drosophila Genetic Reference Panel Transcriptional response to Tunicamycin and control conditions was measured at 8 hours of exposure (20 lines) and 20 hours of exposure (8 lines).

2013-04-30 | E-GEOD-46425 | biostudies-arrayexpress

Transcriptomes profile of Solanum tuberosum (St) and Solanum commersonii (Sc) under cold stress and AtCBF3 overexpression.

Project description:St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species. Plants were grown in 16:8 photoperiod. Eight hours after dawn, plants were either transfered to cold or kept in the warn. Wild type S. tuberosum and S. commersonii were grown at 2oC for 2h, 24h and 7 days. Wild type plants grown under warm temperatures for 2h was used as control for 2h cold samples; wild type warm grown plants for 24h were used as controls for 24h and 7 days cold samples. Under warm conditions, S. commersonii 35S::AtCBF3 lines were compared to S. commersonii wild type plants (same thing was done for S. tuberosum).

2011-04-30 | E-GEOD-22449 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data